CCRVB-51: Franchini ALFQAvsALUM For MS
Kate Goldfarbmuren
2025-06-12
Figure 1 (Infection)
Fig 1bcd
Survival Curves
Fig1b
Fig1c
Fig1d
Fig 1e
Supp Figure 1 (Viral load)
Scatterplots vs 3 groups
SuppFig1a
week 1 post infection
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week 2 post infection
SuppFig1c
week 4 post infection
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week 6 post infection
SuppFig1e
week 8 post infection
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week 10 post infection
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week 12 post infection
Figure 2 (Functional Assays in Blood)
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Fig2a
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Fig2e
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Fig2b
Plasma_peptide26gp120_antibody_response__WkPost vs Plasma_AvidityScore_cV2gp120__WkPost
Fig2di
Fig2d
Fig2i
Fig2l
WkPostAndChange
ALUM
14 up and 2 down pairs with p < 0.05
ALFQA
17 up and 0 down pairs with p < 0.05
alluvial (0.05)
Supp Figure 2 (Functional Assays in Blood)
SuppFig2abcdefhi
SuppFig2a
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Plasma_ADCC_Killing__WkPost vs Plasma_gp120_antibody_titers__WkPost
SuppFig2j
Plasma_ADCP_SIVgp120dV1__Change vs Plasma_ADNP_SIVgp120dV1__Change
SuppFig2k
Plasma_Trogocytosis_dV1gp120__Change vs Plasma_ADNP_SIVgp120dV1__Change
SuppFig2l
Plasma_AvidityScore_dV1M766gp120__WkPost vs Plasma_ADNP_SIVgp120dV1__Change
Figure 3 (RM)
Fig3aeh
Fig3a
Fig3e
Fig3h
Fig3b
PBMCs_PctCD14_efferocytes__WkPost vs RectMucosa_CD73posCD163posMacrophages__Change
Fig3cfg
Fig3c
Fig3f
Fig3g
Fig3di
Fig3d
Fig3i
Fig3j
WkPostAndChange
ALUM
24 up and 3 down pairs with p < 0.05
ALFQA
16 up and 1 down pairs with p < 0.05
alluvial (0.05)
Supp Figure 3 (FACS scheme)
FACS scheme
Supp Figure 4 (RM)
SuppFig4bdehi
SuppFig4b
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RectMucosa_CD73posCD163posMacrophages__Change vs Vaginal_secretions_dV1gp120_antibody_titers__WkPost
SuppFig4f
RectMucosa_CD73posCD163posMacrophages__Change vs RectMucosa_CD73posDC10__Change
SuppFig4k
RectMucosa_DC10__WkPost vs RectMucosa_NKp44__WkPost
SuppFig4l
RectMucosa_CD163posMacrophages__Change vs RectMucosa_NKp44__Change
SuppFig4m
RectMucosa_CD163posMacrophages__Change vs RectMucosa_NKp44negNKG2Aneg_PMA_IFNg__Change
SuppFig4n
RectMucosa_CD73posCD163posMacrophages__WkPost vs RectMucosa_NKp44negNKG2Aneg_PMA_IFNg__WkPost
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Plasma_V2specific_ADCC_Killing__WkPost vs RectMucosa_NKp44__Change
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Figure 4 (Plasma cytokines)
Fig4a
ellipse = 95 % normal probability
top 5 loadings per PC displayed
17 ALUM + 12 ALFQA animals in PCA
Fig4b
ellipse = 95 % normal probability
top 5 loadings per PC displayed
12 ALUM + 12 ALFQA animals in PCA
Fig4c
x-axis: log10(abs(MW estimate x100)) x sign of MW estimate
MW estimate = median of outer differences
outer differences = difference between all pairs of values in group1 - group2, e.g. for A = a1, a2 and B = b1, b2; then the outer differences would be: a1-b1, a2-b1, a1-b2, a2-b2. And the MW estimate is the median of these deltas. For MW estimate > 0, ALFQA > ALUM; and for MW estmate < 0, ALFQA < ALUM
x100 = to shift all estimates > 1 (or < -1) so that the log10 does not transform values -1 < x < 1; thus for a MW estimate of 0.01 (the smallest magnitude estimate) –> log10(0.01 x100) = 0
Fig4d
x-axis: log10(abs(MW estimate x100)) x sign of MW estimate
MW estimate = median of outer differences
outer differences = difference between all pairs of values in group1 - group2, e.g. for A = a1, a2 and B = b1, b2; then the outer differences would be: a1-b1, a2-b1, a1-b2, a2-b2. And the MW estimate is the median of these deltas. For MW estimate > 0, ALFQA > ALUM; and for MW estmate < 0, ALFQA < ALUM
x100 = to shift all estimates > 1 (or < -1) so that the log10 does not transform values -1 < x < 1; thus for a MW estimate of 0.01 (the smallest magnitude estimate) –> log10(0.01 x100) = 0
Fig4e
baseline same assays, without Baseline
Fig4fghijk
Fig4f
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Supp Figure 5 (Plasma cytokines)
SuppFig5a
ellipse = 95 % normal probability
top 5 loadings per PC displayed
12 ALUM + 12 ALFQA animals in PCA
SuppFig5b
x-axis: log10(abs(MW estimate x100)) x sign of MW estimate
MW estimate = median of outer differences
outer differences = difference between all pairs of values in group1 - group2, e.g. for A = a1, a2 and B = b1, b2; then the outer differences would be: a1-b1, a2-b1, a1-b2, a2-b2. And the MW estimate is the median of these deltas. For MW estimate > 0, ALFQA > ALUM; and for MW estmate < 0, ALFQA < ALUM
x100 = to shift all estimates > 1 (or < -1) so that the log10 does not transform values -1 < x < 1; thus for a MW estimate of 0.01 (the smallest magnitude estimate) –> log10(0.01 x100) = 0
SuppFig5c
Baseline diff only
SuppFig5d
SuppFig5e
Figure 5 (Plasma cytokines)
Fig5a
Baseline
ALUM
2 up and 0 down pairs with p < 0.001
ALFQA
6 up and 0 down pairs with p < 0.001
alluvial (0.001)
wk12_24h
ALUM
8 up and 0 down pairs with p < 0.001
ALFQA
8 up and 0 down pairs with p < 0.001
alluvial (0.001)
wk13
ALUM
1 up and 0 down pairs with p < 0.001
ALFQA
10 up and 0 down pairs with p < 0.001
alluvial (0.001)
Fig5b
For IPA (see methods)
Fig5c
For IPA (see methods)
Supp Figure 6 (Pathway analysis)
SuppFig6a
For IPA (see methods)
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For IPA (see methods)
Figure 6 (Plasma cytokines & Summary)
Fig 6a
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Fig6c
RectMucosa_DC10__Change vs LTA__wk13
Fig 6e
Summary of variables different ALFQA vs Alum, associations with TOA
Supp Figure 7 (Plasma cytokines & summary)
Supp Fig7a
Supp Fig7b
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RectMucosa_DC10__Change vs MMP12__wk12_24h
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RectMucosa_DC10__Change vs CCL13__wk12_24h
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RectMucosa_DC10__Change vs VEGFA__wk12_24h
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ALUM
ALFQA
Supp Figure 8 (Plasma cytokines & summary)
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CXCL8__wk13 vs EGF__wk13
Supp Fig8e
ALUM
ALFQA
Data tables
Raw Values
Excel spreadsheet of RAW datasetsPlotted Values
Excel spreadsheet of plotted valuesStats
Mann-Whitney/Wilcoxon test between groups at each timepoint
Spearman correlation between TOA and assays, or among assays
Excel spreadsheet of statsSession info
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